It's about time: Signal recognition in staged models of protein translocation

During their synthesis, a large fraction of proteins are directed to the secretory pathway. There are several models that aim to distinguish between different destinations along this pathway; however, they rarely distinguish between known stages of this translocation process.This paper presents a translocation probability function which models the protein SRP-recruitment process—the first stage of the secretory pathway. It unifies groups of proteins with distinct final destinations, allowing more specific sorting to be done in due course, mirroring the hierarchical nature of secretory translocation.We apply conditional random fields to evaluate the prediction accuracy of a full sequence model. Introducing the translocation function improves substantially compared to a model based on properties that are relevant to the subsequent stages and final destinations only. For the discrimination of secretory, signal peptide (SP)-equipped proteins and non-secretory proteins a correlation coefficient of 0.98 is achieved—a level of performance that is only met by specialized SP predictors. Transmembrane proteins cause considerable confusion in signal peptide predictors, but fit naturally into our transparent design and reduce the performance of the translocation function only slightly.The proposed function and model assist efforts to uncover localization and function for the growing numbers of protein sequence data. Applying our model we estimate with high confidence that about 27% of the human and 29% of the mouse proteins are associated with the secretory pathway.     

Time-Optimal Coordination of Flexible Manufacturing Systems Using Deterministic Finite Automata and Mixed Integer Linear Programming

Automation and flexibility are often mentioned as key concepts in modern production industry. To increase the level of flexibility, deterministic finite automata (DFA) can be used to model, specify and verify the production systems. Often, it is also desirable to optimize some production criteria, such as for example the cycle time of a manufacturing cell. In this paper, a method for automatic conversion from DFA to a mixed integer linear programming (MILP) formulation is first presented. This conversion is developed for a number of DFA structures that have shown to be useful in practical applications. Special attention is paid to reducing the search region explored by the MILP solver. Second, a conversion from the MILP solution to a DFA supervisor is described. This allows to combine the advantages of DFA modeling with the efficiency of MILP and supervisory control theory to automatically generate time-optimal, collision-free and non-blocking working schedules for flexible manufacturing systems.

Analyzing Innermost Runtime Complexity of Term Rewriting by Dependency Pairs

We present a modular framework to analyze the innermost runtime complexity of term rewrite systems automatically. Our method is based on the dependency pair framework for termination analysis. In contrast to previous work, we developed a direct adaptation of successful termination techniques from the dependency pair framework in order to use them for complexity analysis. By extensive experimental results, we demonstrate the power of our method compared to existing techniques.     

Cross-system user modeling and personalization on the Social Web

In order to adapt functionality to their individual users, systems need information about these users. The Social Web provides opportunities to gather user data from outside the system itself. Aggregated user data may be useful to address cold-start problems as well as sparse user profiles, but this depends on the nature of individual user profiles distributed on the Social Web. For example, does it make sense to re-use Flickr profiles to recommend bookmarks in Delicious? In this article, we study distributed form-based and tag-based user profiles, based on a large dataset aggregated from the Social Web. We analyze the completeness, consistency and replication of form-based profiles, which users explicitly create by filling out forms at Social Web systems such as Twitter, Facebook and LinkedIn. We also investigate tag-based profiles, which result from social tagging activities in systems such as Flickr, Delicious and StumbleUpon: to what extent do tag-based profiles overlap between different systems, what are the benefits of aggregating tag-based profiles. Based on these insights, we developed and evaluated the performance of several cross-system user modeling strategies in the context of recommender systems. The evaluation results show that the proposed methods solve the cold-start problem and improve recommendation quality significantly, even beyond the cold-start.     

Towards automatic bounding box annotations from weakly labeled images

In this work we discuss the problem of automatically determining bounding box annotations for objects in images whereas we only assume weak labeling in the form of global image labels. We therefore are only given a set of positive images all containing at least one instance of a desired object and a negative set of images which represent background. Our goal is then to determine the locations of the object instances within the positive images by bounding boxes. We also describe and analyze a method for automatic bounding box annotation which consists of two major steps. First, we apply a statistical model for determining visual features which are likely to be indicative for the respective object class. Based on these feature models we infer preliminary estimations for bounding boxes. Second, we use a CCCP training algorithm for latent structured SVM in order to improve the initial estimations by using them as initializations for latent variables modeling the optimal bounding box positions. We evaluate our approach on three publicly available datasets.     

TET-Like Oxidation in 5-Methylcytosine and Derivatives: A Computational and Experimental Study

The epigenetic marker 5-methylcytosine (5mC) is an important factor in DNA modification and epigenetics. It can be modified through a three-step oxidation performed by ten-eleven-translocation (TET) enzymes and we have previously reported that the iron(IV)-oxo complex [Fe(O)(Py₅Me₂H)]²⁺ ( 1 ) can oxidize 5mC. Here, we report the reactivity of this iron(IV)-oxo complex towards a wider scope of methylated cytosine and uracil derivatives relevant for synthetic DNA applications, such as 1-methylcytosine (1mC), 5-methyl-iso-cytosine (5miC) and thymine (T/5mU). The observed kinetic parameters are corroborated by calculation of the C−H bond energies at the reactive sites which was found to be an efficient tool for reaction rate prediction of 1 towards methylated DNA bases. We identified oxidation products of methylated cytosine derivatives using HPLC-MS and GC-MS. Thereby, we shed light on the impact of the methyl group position and resulting C−H bond dissociation energies on reactivity towards TET-like oxidation.     

驾驭自然资源

海上风电作为便宜且可再生的能源，世界各国政府都希望能对其加以利用。然而，在海洋环境中开发风电场会面临一系列新的工程挑战。比如说，在设计海上风力涡轮机支撑结构时，支撑结构必须能够承载着大型风力涡轮机在深水环境中正常运转。在设计这种成本效益型且可靠的海上风力涡轮机大型结构时，工程仿真就成了宝贵的工具。     

I'm home: Defining and evaluating a gesture set for smart-home control

Mobile phones seem to present the perfect user interface for interacting with smart environments, e.g. smart-home systems, as they are nowadays ubiquitous and equipped with an increasing amount of sensors and interface components, such as multi-touch screens. After giving an overview on related work this paper presents the adapted design methodology proposed by Wobbrock et al. (2009) for the development of a gesture-based user interface to a smart-home system. The findings for the new domain, device and gesture space are presented and compared to findings by Wobbrock et al. (2009). Three additional steps are described: A small pre-test survey, a mapping and a memory test and a performance test of the implemented system.This paper shows the adaptability of the approach described by Wobbrock et al. (2009) for three-dimensional gestures in the smart-home domain. Elicited gestures are described and a first implementation of a user interface based on these gestures is presented.